[gmx-users] some problems by freshman

[David van der Spoel]

On Fri, 2002-08-16 at 10:27, zpxu wrote:
> Dear All:
>     I am wondering if you can show me such fundamental things:
> 1) I want L-J interaction only between the C_I(innertube) and C_O(outertube)
> atoms (two type of atoms in one molecule).
>     and their are four sections concern L-J potential.
>     a)section [atomtypes] in topology file
>     b)section [nonbond_params] in topology file
>     c)section [pairtypes] in topology file
>     d)section [pairs] in topology file
>     now I only use b).
>     is it ok?
You must define the atom types in a), but you can set the parameters in
b) if you like.

> 2) the unit of potential parameters, I use nm,kJ/mol
>     is it ok?
Yes

> 3) my coordinate is at nanometer scale, so I shift it by 3nm, let the tubes
> in box.
Yes

>     
> 4) I set charge to zero, and set charge group arbitrarily.will it be ok?
Set them all to the atom number
> 
> 
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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